University of Nebraska Medical Center DigitalCommons@UNMC Theses & Dissertations Graduate Studies Fall 12-14-2018 Development of Preclinical Magnetic Resonance Imaging Relational Database and Interactive Analytical Tool for Diffusion Tensor Imaging Ahmad Tanwir University of Nebraska Medical Center Follow this and additional works at: https://digitalcommons.unmc.edu/etd Recommended Citation Tanwir, Ahmad, "Development of Preclinical Magnetic Resonance Imaging Relational Database and Interactive Analytical Tool for Diffusion Tensor Imaging" (2018). Theses & Dissertations. 332. https://digitalcommons.unmc.edu/etd/332 This Thesis is brought to you for free and open access by the Graduate Studies at DigitalCommons@UNMC. It has been accepted for inclusion in Theses & Dissertations by an authorized administrator of DigitalCommons@UNMC. For more information, please contact [email protected]. Development of Preclinical Magnetic Resonance Imaging Relational Database and Interactive Analytical Tool for Diffusion Tensor Imaging by Ahmad Tanwir A THESIS Presented to the Faculty of the University of Nebraska Graduate College in Partial Fulfillment of the Requirements for the Degree of Master of Science Biomedical Informatics Graduate Program Under the Supervision of Prof. Chittibabu Guda and Dr. Balasrinivasa R. Sajja University of Nebraska Medical Center Omaha, Nebraska November, 2018 Supervisory Committee: Dr. Peter Wolcott Dr. Mahbubul A Majumder ACKNOWLEDGEMENT First of all, I am grateful to my God for the good health and wellbeing that were necessary to complete this long journey. I am especially indebted to my supervisors, Prof. Chittibabu Guda and Dr. Balasrinivasa R. Sajja, for all the selfless time, wisdom, care, and unparalleled support that kept me going. Their unwavering guidance helped me in all the time of research and writing of this thesis. I whole-heartedly express my sincere thanks to all the members of my supervisory committee, Dr. Peter Wolcott and Dr. Mahbubul A Majumder, not only for their insightful comments and encouragement, but also for the critical question, which incented me to widen my research from various perspectives. I would like express gratitude to all the members of Bio-imaging core facility. I specially thank Dr. Yutong Liu, Melissa Mellon, Dr. Mariano Uberti, and Dr. Lirong Xu for their helps and supports. Besides that I would like to remember my first supervisor late Prof. Michael D. Boska for his contribution to change my philosophy about the life and science. I also thank my parents, late Prof. Ruhul Amin and Kohinoor Begum and my in- laws for the unceasing encouragement, support and endless prayer from 8000 miles away from USA. Last, but not the least, I am grateful and dedicate this thesis to my life-partner, Rahat Jahan who supported me each and every moment and being patient more than me throughout this entire journey. I can clearly shout that, without her tremendous devotion and sacrifices, the journey would not be possible at all. Lastly, I thank my 2.9 years old son, Umair Ahmad for being the most lovable and understanding boy ever in the universe. Development of Preclinical Magnetic Resonance Imaging Relational Database and Interactive Analytical Tool for Diffusion Tensor Imaging Ahmad Tanwir, M.S. University of Nebraska Medical Center, 2018 Co-Advisors: Chittibabu Guda, Ph.D. and Balasrinivasa R. Sajja, Ph.D. Databases have become an essential component for any organization to collect and manage the information. Similar to other domains, by implementing a database management system (DBMS), data storage, access, analysis and updates can be automated and optimized in the biological, medical and preclinical research areas. This work demonstrated the development of a preclinical database, which contains the processed results from different magnetic resonance imaging (MRI) techniques with relevant biological information. In addition, we designed and implemented an interactive analytical tool to format and analyze diffusion tensor imaging (DTI) data and automatically generate results in the forms of box plot, bar plot, line plot with statistical summary. The performance of the newly built analytical tool was tested to determine the accuracy and robustness by following functional-unit test procedures. Microsoft SQL Server 2016 Express edition was used to develop the database, and an open source programming language R was used to develop the interactive analytical tool. Results showed that implementation of DBMS and the interactive analytical tool has drastically reduced data analysis time. While the conventional analytical method required more than three days to format, process, analyze and produce results from one study dataset, the DTI analytical tool returned the same results within 10 minutes. This database and the accompanying tool will be very effective for enhancing the speed of data analysis of diffusion tensor imaging data. i TABLE OF CONTENTS LIST OF FIGURES ......................................................................................................... iii LIST OF TABLES .......................................................................................................... vii LIST OF ABBREVIATIONS .......................................................................................... viii CHAPTER 1: INTRODUCTION ...................................................................................... 1 1.1 Database .............................................................................................................. 2 1.1.1 Data model ..................................................................................................... 3 1.1.1.1 Conceptual Data Model ............................................................................ 3 1.1.1.2 Logical Data Model .................................................................................. 4 1.1.1.3 Physical Data Model ................................................................................ 4 1.1.2 Database models ............................................................................................ 5 1.1.2.1 Relational Model ...................................................................................... 6 1.1.2.2 Entity Relationship Model ......................................................................... 7 1.2 Diffusion Tensor Imaging ...................................................................................... 8 1.2.1 Principles of Diffusion Tensor Imaging ............................................................ 9 1.2.1.1 Diffusion Weighted Imaging ..................................................................... 9 1.2.1.2 Diffusion Tensor Imaging ........................................................................12 1.2.2 Scalar Invariants from the Diffusion Tensor ...................................................14 1.2.2.1 Trace and Mean Diffusivity ......................................................................14 1.2.2.3 Fractional Anisotropy ..............................................................................15 1.2.2.4 Relative Anisotropy .................................................................................15 1.2.3 DTI Data Processing......................................................................................16 1.3 Structure of the Thesis .........................................................................................17 CHAPTER 2: METHODS AND MATERIALS .................................................................19 2.1. Development of a Relational Database for DTI data............................................19 2.1.1. Requirements Collection ...............................................................................19 2.1.2. Design of Tables in the Database .................................................................21 ii 2.1.2. Logical Model Design ...................................................................................22 2.1.3. Physical Model Design .................................................................................26 2.2. Design and implementation of an interactive tool for analyzing DTI measures ....27 2.2.1. Data Formatting Tab Set ..............................................................................30 2.2.2. Data Extraction Tab Set ................................................................................32 2.2.3. Data Visualization Tab Set............................................................................33 2.2.4. Statistical Analysis Tab Set...........................................................................36 2.2.5 Quality Assurance of the DTI Interactive Tool ................................................39 2.3. Test Dataset Creation .........................................................................................49 2.3.1. Experimental Study Design...........................................................................49 2.3.2. DTI Data Processing.....................................................................................50 CHAPTER 3: RESULTS ................................................................................................52 CHAPTER 4: DISCUSSION ..........................................................................................72 REFERENCES ..............................................................................................................75 APPENDIX A .................................................................................................................78